The Venezuelan judge Maria Lourdes Afiuni, who was jailed after granting bail to a banker who later fled. Photograph: Reuters

Hugo Chávez's long-time supporter Noam Chomsky has issued a renewed appeal to the Venezuelan president to free a judge who was controversially jailed two years ago, prompting criticism from human rights activists and academics.

Maria Lourdes Afiuni, 48, has been imprisoned since December 2009 and is currently under house arrest in the capital, Caracas.

In an open letter to the Venezuelan president, Chomsky, a linguistics professor from the Massachusetts Institute of Technology, urged Chávez to "correct an injustice".

"This is an appeal for the release of Judge Afiuni on humanitarian grounds after two years," Chomsky told the Guardian on Wednesday in a telephone interview. "As the letter says I hope President Chávez will release her. Presumably these are regular Christmas pardons."

Activists, including Chomsky, have made repeated calls for Afiuni's release, partly on the grounds of ill health. Afiuni is a cancer patient who underwent an abdominal hysterectomy while in jail.

"President Chávez himself is in a courageous fight against cancer. For this reason, he is certainly in a position to personally understand the importance of receiving adequate treatment and marshalling your inner strength for survival," Chomsky writes in his latest letter.

"The Christmas-time pardons are an appropriate occasion for President Chávez to correct an injustice and avoid greater damage to her health by a humanitarian release," he added.

Afiuni's troubles began on 10 December 2009 when she granted bail to Eligio Cedeño, a businessman and banker with ties to the Venezuelan opposition. Cedeño had been jailed on charges that he had evaded currency controls and, on release, fled to the United States.

Afiuni's ruling triggered a furious public reaction from the president. Chávez took to the airwaves claiming the judge deserved 30 years in prison and suggesting that in another era she would have been hauled before a firing squad.

"This judge should get the maximum penalty … that judge has to pay for what she has done," he said.

In February this year – following a barrage of criticism from human rights groups including Amnesty International and Human Rights Watch – Afiuni was transferred from the prison to her home, where she has remained under house arrest.

"We don't expect much because this country's justice system is biased," the judge's brother, Nelson Afiuni, said this month. "Most prosecutors and judges respond to the interests of the government, and it's clear the government wants my sister to remain isolated."

In his latest letter Chomsky highlighted the physical suffering that Afiuni, who is a single mother, is said to have undergone in jail.

While in prison Afiuni "experienced grave abuses that led to a severe deterioration of her physical and psychological condition", the American linguist wrote.

While the judge was now under house arrest, "she is prohibited from speaking to the press and from receiving solar rays".

Chomsky added: "After more than two years in custody, there are no guarantees of a fair trial. I am convinced that Judge Afiuni has suffered enough and should be released."

Chomsky's letter is part of a renewed but diplomatically worded push for Afiuni's release.

Speaking to the Guardian on Wednesday, Charlie Clements, director of Harvard's Carr Centre for Human Rights Policy, said: "We hope that given that this is the time of year that the president makes pardons, and that he himself was released under this same scheme, he decides to free her."

"I sincerely hope that the judge and her daughter don't have to suffer any longer," added Clements, who said he was speaking in a personal capacity. "For the Venezuelan judicial system this should come as an international embarrassment."

Leonardo Vivas, a fellow at the Carr centre, described the latest appeal as "a very cordial call for Afiuni to be freed on humanitarian grounds".

"We don't know what the reaction will be," he added.

Despite his appeal for Afiuni's release, Chomsky has been critical of the media's coverage of the case. On Wednesday he suggested the case had received so much media attention only "because Venezuela is an official enemy" [of the United States].

"I am involved in these appeals all the time but I get no calls unless it is an enemy of the US," Chomsky said. "This is more a comment on the media than on the case."